Fix omerotools

[loicsauteur]

PR for issue #154

• Removes unnecessary code in parse_url
• Updates description of parse_url
• Fixes some typos
• Raises FileNotFoundError for upload_image_to_omero

All changes done with no testing. I was unable to create an env from poetry (sorry).

[ehrenfeu]

Thanks @loicsauteur! ❤️

🧾 An issue like this definitely reveals the need for being able to to run tests on the code.

Since we can't properly emulate the fr.igred.omero.Client behavior without a lot of potentially error-prone 🤯 mocking, I'd prefer to rewrite the entire function such that it first does all the string parsing and list assembling (in a separate function*) and only at the very end does the required client.getDataset() / client.getImage() calls.

(*that separate function should be string-based only, making it approachable for pytest 🧪)

Would you like to work on it, otherwise I'd put it onto our list for the next Coding 🧑‍💻 Session (you're welcome to join if you wish)?

[ehrenfeu]

I prefer having separate commits for unrelated changes like fixing typos in docstrings as otherwise the git history if this very line will read Update parse_url description & remove unnecessary code which can be quite confusing.

[ehrenfeu]

This doesn't seem to be very pythonic to me - what happens if this check is not present but the importImage() call is performed on a non-existing file.

Shouldn't it raise a similar exception already, or is this something weird due to the Java stuff going on in the call?

[loicsauteur]

If the file does not exist it throws:

File "__pyclasspath__/imcflibs/imagej/omerotools.py", line 178, in upload_image_to_omero
IndexError: index out of range: 0

importImage() should throw an IOException but not fully clear where... the library is very convoluted... see here if you like.

If by pythonic you mean something else, happy to get your inputs.

[ehrenfeu]

Ah okay, this does makes sense.

An IndexError is not what you'd expect when a file is missing. Although in this case that's simply due to the [0] at the end of that all-in-one return line.

I'm fine leaving it like this for now, but please add a comment to the if statement explaining this.

[loicsauteur]

I'd welcome the opportunity to join one of your coding sessions and work on this.

As I am not really used to working on a collaborative project, I'm happy about the pointers and how-to. E.g.:

• how-to comment on a commit with more than the commit message

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 33%. Comparing base (bc94ec9) to head (8c5ac37).

Additional details and impacted files

@@          Coverage Diff          @@
##           master   #157   +/-   ##
=====================================
  Coverage      33%    33%           
=====================================
  Files          25     25           
  Lines        1806   1805    -1     
=====================================
  Hits          591    591           
+ Misses       1215   1214    -1     

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[loicsauteur]

I added the refactoring of the parse_url:

2 additional functions with their tests (in test_omerotools.py)

I also added a very basic test function for parse_url itself, but it only tests the first part of the function (for the expected risen errors).

Important: I have not tested the modified parse_url function in Fiji or similar...